##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(shape=espressomd.shapes.Cylinder(center=0.5 * BOX_L,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
wall = LBBoundary(shape=espressomd.shapes.Wall(dist=PADDING, normal=[1, 0, 0]))
system.lbboundaries.add(wall)
wall = LBBoundary(
shape=espressomd.shapes.Wall(dist=-(LENGTH + PADDING), normal=[-1, 0, 0]))
system.lbboundaries.add(wall)
# Setup cone
IRAD = 4.0
ANGLE = np.pi / 4.0
os.remove(os.path.join(checkpoint.checkpoint_dir, filepath))
LB_implementation = None
if 'LB.CPU' in modes:
LB_implementation = espressomd.lb.LBFluid
elif 'LB.GPU' in modes and espressomd.gpu_available():
LB_implementation = espressomd.lb.LBFluidGPU
if LB_implementation:
lbf = LB_implementation(agrid=0.5, visc=1.3, dens=1.5, tau=0.01)
system.actors.add(lbf)
if 'THERM.LB' in modes:
system.thermostat.set_lb(LB_fluid=lbf, seed=23, gamma=2.0)
if any(has_features(i) for i in ["LB_BOUNDARIES", "LB_BOUNDARIES_GPU"]):
if 'EK.GPU' not in modes:
system.lbboundaries.add(
LBBoundary(shape=Wall(normal=(0, 0, 1), dist=0.5),
velocity=(1e-4, 1e-4, 0)))
EK_implementation = None
if 'EK.GPU' in modes and espressomd.gpu_available(
) and espressomd.has_features('ELECTROKINETICS'):
EK_implementation = espressomd.electrokinetics
ek = EK_implementation.Electrokinetics(agrid=0.5,
lb_density=26.15,
viscosity=1.7,
friction=0.0,
T=1.1,
prefactor=0.88,
stencil="linkcentered")
ek_species = EK_implementation.Species(
density=0.4,
D=0.02,
system.actors.add(lbf)
##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(
shape=Cylinder(
center=BOX_L / 2.,
axis=[1, 0, 0], radius=DIAMETER / 2.0, length=LENGTH, direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
## Exercise 1 ##
# Set up two walls to cap the cylinder respecting the padding
# between them and the edge of the box, with a normal along the x-axis
wall = ...
# Setup cone
IRAD = 4.0
ANGLE = pi / 4.0
ORAD = (DIAMETER - IRAD) / sin(ANGLE)
system.thermostat.set_lb(LB_fluid=lbf, gamma=frict, seed=42)
################################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(
shape=Cylinder(
center=[length / 2.0, (diameter + 4) / 2.0, (diameter + 4) / 2.0],
axis=[1, 0, 0], radius=diameter / 2.0, length=length, direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
## Exercise 1 ##
# Set up two walls to cap the cylinder a distance of 2 away
# from the edge of the box, with a normal along the x-axis
wall = ...
# Setup cone
irad = 4.0
angle = pi / 4.0
orad = (diameter - irad) / sin(angle)
system.actors.add(lbf)
##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(
shape=espressomd.shapes.Cylinder(
center=BOX_L / 2.,
axis=[1, 0, 0], radius=DIAMETER / 2.0, length=LENGTH, direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
## Exercise 1 ##
# Set up two walls to cap the cylinder respecting the padding
# between them and the edge of the box, with a normal along the x-axis
wall = LBBoundary(shape=espressomd.shapes.Wall(...), ...)
# Setup cone
IRAD = 4.0
ANGLE = np.pi / 4.0
ORAD = (DIAMETER - IRAD) / np.sin(ANGLE)
SHIFT = 0.25 * ORAD * np.cos(ANGLE)
##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(shape=Cylinder(center=BOX_L / 2.,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
## Exercise 1 ##
# Set up two walls to cap the cylinder respecting the padding
# between them and the edge of the box, with a normal along the x-axis
wall = ...
# Setup cone
IRAD = 4.0
ANGLE = pi / 4.0
##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(shape=Cylinder(center=0.5 * BOX_L,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
wall = LBBoundary(shape=Wall(dist=PADDING, normal=[1, 0, 0]))
system.lbboundaries.add(wall)
wall = LBBoundary(shape=Wall(dist=-(LENGTH + PADDING), normal=[-1, 0, 0]))
system.lbboundaries.add(wall)
# Setup cone
IRAD = 4.0
################################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create an cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
################################################################################
# Setup cylinder
cylinder = LBBoundary(shape=Cylinder(
center=[length / 2.0, (diameter + 4) / 2.0, (diameter + 4) / 2.0],
axis=[1, 0, 0],
radius=diameter / 2.0,
length=length,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
## Exercise 1 ##
# Set up two walls to cap the cylinder a distance of 2 away
# from the edge of the box, with a normal along the x-axis
wall = ...
# Setup cone
irad = 4.0
angle = pi / 4.0
##########################################################################
#
# Now we set up the three LB boundaries that form the rectifying geometry.
# The cylinder boundary/constraint is actually already capped, but we put
# in two planes for safety's sake. If you want to create a cylinder of
# 'infinite length' using the periodic boundaries, then the cylinder must
# extend over the boundary.
#
##########################################################################
# Setup cylinder
cylinder = LBBoundary(shape=Cylinder(center=0.5 * BOX_L,
axis=[1, 0, 0],
radius=DIAMETER / 2.0,
length=LENGTH,
direction=-1))
system.lbboundaries.add(cylinder)
# Setup walls
wall = LBBoundary(shape=Wall(dist=PADDING, normal=[1, 0, 0]))
system.lbboundaries.add(wall)
wall = LBBoundary(shape=Wall(dist=-(LENGTH + PADDING), normal=[-1, 0, 0]))
system.lbboundaries.add(wall)
# Setup cone
IRAD = 4.0
